2df4 - Revision history

OCA at 08:26, 25 October 2023

2023-10-25T08:26:18Z

← Older revision		Revision as of 08:26, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='2df4' size='340' side='right'caption='[[2df4]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='2df4' size='340' side='right'caption='[[2df4]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2df4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus~~ aureus~~" (rosenbach 1884) zopf 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DF4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2df4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DF4 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>~~		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.2Å</td></tr>
	~~<tr id='related'><td class="sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[2f2a\|2f2a]]~~, [[~~2g5h~~\|~~2g5h~~]]~~, [[2g5i\|2g5i]]</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>gatA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1280~~ "~~Micrococcus aureus~~" ~~(Rosenbach 1884) Zopf 1885]), gatB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=1280 "Micrococcus aureus"~~ (~~Rosenbach 1884~~) ~~Zopf 1885]), gatC ([https:~~/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])~~</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2df4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df4 OCA], [https://pdbe.org/2df4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2df4 RCSB], [https://www.ebi.ac.uk/pdbsum/2df4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2df4 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2df4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df4 OCA], [https://pdbe.org/2df4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2df4 RCSB], [https://www.ebi.ac.uk/pdbsum/2df4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2df4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/GATA_STAAM GATA_STAAM]] Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln) (By similarity). [[https://www.uniprot.org/uniprot/GATC_STAAM GATC_STAAM]] Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) (By similarity). [[https://www.uniprot.org/uniprot/GATB_STAAM GATB_STAAM]] Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) (By similarity).		[https://www.uniprot.org/uniprot/GATA_STAAM GATA_STAAM] Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln) (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Nakamura, A~~]]		[[Category: Staphylococcus aureus]]
	[[Category: ~~Tanaka, I~~]]		[[Category: Nakamura A]]
	[[Category: ~~Yao, M~~]]		[[Category: Tanaka I]]
	[[Category: ~~Ligase]]~~		[[Category: Yao M]]
	~~[[Category: Multi protein complex~~]]

OCA at 12:01, 3 February 2021

2021-02-03T12:01:23Z

← Older revision		Revision as of 12:01, 3 February 2021
Line 1:		Line 1:

	==Structure of tRNA-Dependent Amidotransferase GatCAB complexed with Mn2+==		==Structure of tRNA-Dependent Amidotransferase GatCAB complexed with Mn2+==
	<StructureSection load='2df4' size='340' side='right' caption='[[2df4]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='2df4' size='340' side='right'caption='[[2df4]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2df4]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DF4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2df4]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DF4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f2a\|2f2a]], [[2g5h\|2g5h]], [[2g5i\|2g5i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2f2a\|2f2a]], [[2g5h\|2g5h]], [[2g5i\|2g5i]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gatA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885]), gatB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885]), gatC ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gatA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885]), gatB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885]), gatC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2df4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df4 OCA], [~~http~~://pdbe.org/2df4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2df4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2df4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2df4 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2df4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df4 OCA], [https://pdbe.org/2df4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2df4 RCSB], [https://www.ebi.ac.uk/pdbsum/2df4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2df4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/GATA_STAAM GATA_STAAM]] Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln) (By similarity). [[~~http~~://www.uniprot.org/uniprot/GATC_STAAM GATC_STAAM]] Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) (By similarity). [[~~http~~://www.uniprot.org/uniprot/GATB_STAAM GATB_STAAM]] Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) (By similarity).		[[https://www.uniprot.org/uniprot/GATA_STAAM GATA_STAAM]] Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln) (By similarity). [[https://www.uniprot.org/uniprot/GATC_STAAM GATC_STAAM]] Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) (By similarity). [[https://www.uniprot.org/uniprot/GATB_STAAM GATB_STAAM]] Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 2df4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2df4" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Glutamyl-tRNA(Gln) amidotransferase\|Glutamyl-tRNA(Gln) amidotransferase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Nakamura, A]]		[[Category: Nakamura, A]]
	[[Category: Tanaka, I]]		[[Category: Tanaka, I]]

OCA at 06:36, 30 May 2018

2018-05-30T06:36:43Z

← Older revision		Revision as of 06:36, 30 May 2018
Line 1:		Line 1:

	==Structure of tRNA-Dependent Amidotransferase GatCAB complexed with Mn2+==		==Structure of tRNA-Dependent Amidotransferase GatCAB complexed with Mn2+==
	<StructureSection load='2df4' size='340' side='right' caption='[[2df4]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='2df4' size='340' side='right' caption='[[2df4]], [[Resolution\|resolution]] 3.20Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f2a\|2f2a]], [[2g5h\|2g5h]], [[2g5i\|2g5i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f2a\|2f2a]], [[2g5h\|2g5h]], [[2g5i\|2g5i]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gatA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885]), gatB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885]), gatC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gatA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885]), gatB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885]), gatC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2df4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df4 OCA], [http://pdbe.org/2df4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2df4 RCSB], [http://www.ebi.ac.uk/pdbsum/2df4 PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2df4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df4 OCA], [http://pdbe.org/2df4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2df4 RCSB], [http://www.ebi.ac.uk/pdbsum/2df4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2df4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/2df4_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/2df4_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 22:04, 8 February 2016

2016-02-08T22:04:21Z

← Older revision		Revision as of 22:04, 8 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2df4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:48, 10 September 2015

2015-09-10T15:48:12Z

← Older revision		Revision as of 15:48, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2df4' size='340' side='right' caption='[[2df4]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='2df4' size='340' side='right' caption='[[2df4]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2df4]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Staphylococcus_aureus Staphylococcus~~ aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DF4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2df4]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DF4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f2a\|2f2a]], [[2g5h\|2g5h]], [[2g5i\|2g5i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f2a\|2f2a]], [[2g5h\|2g5h]], [[2g5i\|2g5i]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gatA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 ~~Staphylococcus~~ aureus]), gatB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 ~~Staphylococcus~~ aureus]), gatC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 ~~Staphylococcus~~ aureus])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gatA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885]), gatB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885]), gatC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2df4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2df4 RCSB], [http://www.ebi.ac.uk/pdbsum/2df4 PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2df4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df4 OCA], [http://pdbe.org/2df4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2df4 RCSB], [http://www.ebi.ac.uk/pdbsum/2df4 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2df4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Staphylococcus aureus]]~~
	[[Category: Nakamura, A]]		[[Category: Nakamura, A]]
	[[Category: Tanaka, I]]		[[Category: Tanaka, I]]

OCA at 02:26, 25 December 2014

2014-12-25T02:26:21Z

← Older revision		Revision as of 02:26, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2df4]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DF4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2df4]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DF4 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f2a\|2f2a]], [[2g5h\|2g5h]], [[2g5i\|2g5i]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f2a\|2f2a]], [[2g5h\|2g5h]], [[2g5i\|2g5i]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gatA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus]), gatB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus]), gatC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gatA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus]), gatB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus]), gatC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2df4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2df4 RCSB], [http://www.ebi.ac.uk/pdbsum/2df4 PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2df4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2df4 RCSB], [http://www.ebi.ac.uk/pdbsum/2df4 PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/GATA_STAAM GATA_STAAM]] Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln) (By similarity). [[http://www.uniprot.org/uniprot/GATC_STAAM GATC_STAAM]] Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) (By similarity). [[http://www.uniprot.org/uniprot/GATB_STAAM GATB_STAAM]] Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
	[[Category: Nakamura, A.]]		[[Category: Nakamura, A]]
	[[Category: Tanaka, I.]]		[[Category: Tanaka, I]]
	[[Category: Yao, M.]]		[[Category: Yao, M]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: Multi protein complex]]		[[Category: Multi protein complex]]

OCA at 02:47, 30 September 2014

2014-09-30T02:47:32Z

← Older revision		Revision as of 02:47, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2df4~~.~~png~~\|~~left~~\|~~200px~~]]		==Structure of tRNA-Dependent Amidotransferase GatCAB complexed with Mn2+==
			<StructureSection load='2df4' size='340' side='right' caption='[[2df4]], [[Resolution\|resolution]] 3.20Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2df4]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DF4 FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2f2a\|2f2a]], [[2g5h\|2g5h]], [[2g5i\|2g5i]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gatA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus]), gatB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus]), gatC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 Staphylococcus aureus])</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2df4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2df4 RCSB], [http://www.ebi.ac.uk/pdbsum/2df4 PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/2df4_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The formation of glutaminyl transfer RNA (Gln-tRNA(Gln)) differs among the three domains of life. Most bacteria employ an indirect pathway to produce Gln-tRNA(Gln) by a heterotrimeric glutamine amidotransferase CAB (GatCAB) that acts on the misacylated Glu-tRNA(Gln). Here, we describe a series of crystal structures of intact GatCAB from Staphylococcus aureus in the apo form and in the complexes with glutamine, asparagine, Mn2+, and adenosine triphosphate analog. Two identified catalytic centers for the glutaminase and transamidase reactions are markedly distant but connected by a hydrophilic ammonia channel 30 A in length. Further, we show that the first U-A base pair in the acceptor stem and the D loop of tRNA(Gln) serve as identity elements essential for discrimination by GatCAB and propose a complete model for the overall concerted reactions to synthesize Gln-tRNA(Gln).

	~~{{STRUCTURE_2df4\| PDB=2df4 \| SCENE= }}~~		Ammonia channel couples glutaminase with transamidase reactions in GatCAB.,Nakamura A, Yao M, Chimnaronk S, Sakai N, Tanaka I Science. 2006 Jun 30;312(5782):1954-8. PMID:16809541<ref>PMID:16809541</ref>

	~~===Structure~~ of ~~tRNA-Dependent Amidotransferase GatCAB complexed with Mn2+===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16809541}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2df4]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Staphylococcus_aureus Staphylococcus aureus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DF4 OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:016809541<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
	[[Category: Nakamura, A.]]		[[Category: Nakamura, A.]]

OCA: Protected "2df4" [edit=sysop:move=sysop]

2013-01-06T11:58:55Z

Protected "2df4" [edit=sysop:move=sysop]

← Older revision	Revision as of 11:58, 6 January 2013
(No difference)

OCA at 11:58, 6 January 2013

2013-01-06T11:58:52Z

← Older revision		Revision as of 11:58, 6 January 2013
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:2df4.png\|left\|200px]]		[[Image:2df4.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2df4", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2df4\| PDB=2df4 \| SCENE= }}		{{STRUCTURE_2df4\| PDB=2df4 \| SCENE= }}

	===Structure of tRNA-Dependent Amidotransferase GatCAB complexed with Mn2+===		===Structure of tRNA-Dependent Amidotransferase GatCAB complexed with Mn2+===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16809541}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16809541 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16809541}}		{{ABSTRACT_PUBMED_16809541}}

	==About this Structure==		==About this Structure==
	~~2DF4~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF4 OCA].		[[2df4]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF4 OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16809541~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016809541</ref><references group="xtra"/>
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
	[[Category: Nakamura, A.]]		[[Category: Nakamura, A.]]
	[[Category: Tanaka, I.]]		[[Category: Tanaka, I.]]
	[[Category: Yao, M.]]		[[Category: Yao, M.]]
			[[Category: Ligase]]
	[[Category: Multi protein complex]]		[[Category: Multi protein complex]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 03:52:00 2009''~~

OCA at 01:52, 17 February 2009

2009-02-17T01:52:00Z

← Older revision		Revision as of 01:52, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2DF4 is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF4 OCA].		2DF4 is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF4 OCA].

	==Reference==		==Reference==
	~~Ammonia channel couples glutaminase with transamidase reactions in GatCAB., Nakamura A, Yao M, Chimnaronk S, Sakai N, Tanaka I, Science. 2006 Jun 30;312(5782):1954-8.~~ PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~16809541 16809541]~~		<ref group="xtra">PMID:16809541</ref><references group="xtra"/>
	~~[[Category: Protein complex]]~~
	[[Category: Staphylococcus aureus]]		[[Category: Staphylococcus aureus]]
	[[Category: Nakamura, A.]]		[[Category: Nakamura, A.]]
Line 31:		Line 30:
	[[Category: Multi protein complex]]		[[Category: Multi protein complex]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 07~~:14:~~49 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 03:52:00 2009''